In quantitative analysis of environmental samples using high-performance liquid chromatography–electrospray ionization mass spectrometry (HPLC-ESI-MS) one of the major problems is the suppression or, less frequently, the enhancement of the analyte signals in the presence of matrix components. Standard addition is the most suitable method for compensating matrix effects, but it is time-consuming and laborious. In this study we compare the potential of three calibration approaches to compensate matrix effects that occurred when seven analytes (naphthalene sulfonates) were quantified in time series samples of waters with different matrices (untreated and treated industrial wastewater). The data obtained by external calibration, internal calibration with one standard, and external sample calibration (corresponding to matrix-matched calibration) were compared with those obtained by standard addition. None of the three approaches were suitable for a sample series of highly loaded, untreated wastewater with highly variable matrix. For less heavily loaded and less variable samples (treated wastewater effluents), the external sample calibration provided reasonable results for most analytes with deviations mostly below 25% as compared to standard addition. External sample calibration can be suitable to compensate matrix effects from moderately loaded samples with more uniform matrices, but it is recommended to verify this for each sample series against the standard addition approach.